EDIT 11/16/2012: The original developer of MMD ceased support for the software in 2011. The program still works and is widely used by many fans. However, a new alternative is available by the name of MikuMikuMoving. More info here: [Link]

EDIT 6/3/2013: MikuMikuDance was updated by its creator to version 7.39ｍ. More info here: [Link]